src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.gui.AlignFrame;
   4 import jalview.ws.WSMenuEntryProviderI;
   5 import jalview.ws.api.ServiceWithParameters;
   6 import jalview.ws.jws2.PreferredServiceRegistry;
   7
   8 import java.beans.PropertyChangeSupport;
   9 import java.io.IOError;
  10 import java.io.IOException;
  11 import java.net.URISyntaxException;
  12 import java.util.ArrayList;
  13 import java.util.List;
  14
  15 import javax.swing.JMenu;
  16
  17 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  18 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  19
  20 public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
  21 {
  22   private static SlivkaWSDiscoverer instance = null;
  23
  24   private SlivkaClient slivkaClient;
  25
  26   private SlivkaWSDiscoverer()
  27   {
  28     try
  29     {
  30       slivkaClient = new SlivkaClient(
  31               "gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  32     } catch (URISyntaxException e)
  33     {
  34       throw new RuntimeException(e);
  35     }
  36   }
  37
  38   public static SlivkaWSDiscoverer getInstance()
  39   {
  40     if (instance == null)
  41     {
  42       instance = new SlivkaWSDiscoverer();
  43     }
  44     return instance;
  45   }
  46
  47   List<ServiceWithParameters> getServiceInstances()
  48   {
  49     List<ServiceWithParameters> instances = new ArrayList<>();
  50     for (SlivkaService service : services)
  51     {
  52       for (String classifier : service.classifiers)
  53       {
  54         if (classifier.contains("Multiple sequence alignment"))
  55         {
  56           instances
  57                   .add(new SlivkaMsaServiceInstance(slivkaClient, service));
  58         }
  59         else if (classifier.contains("Protein sequence analysis"))
  60         {
  61           instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
  62                   service, false));
  63         }
  64         else if (classifier
  65                 .contains("Sequence alignment analysis (conservation)"))
  66         {
  67           instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
  68                   service, true));
  69         }
  70
  71       }
  72     }
  73     return instances;
  74   }
  75
  76   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
  77           this);
  78
  79   @Override
  80   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  81   {
  82     JMenu slivkaMenu = new JMenu("Slivka");
  83     wsmenu.add(slivkaMenu);
  84
  85     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  86     slivkaMenu.add(alignmentMenu);
  87     JMenu disorderMenu = new JMenu("Protein sequence analysis");
  88     slivkaMenu.add(disorderMenu);
  89     JMenu conservationMenu = new JMenu("Conservation");
  90     slivkaMenu.add(conservationMenu);
  91     PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
  92             getServiceInstances(),
  93               changeSupport, slivkaMenu, alignFrame, null);
  94
  95   }
  96
  97   List<SlivkaService>services=null;
  98
  99   volatile boolean started = false, finished = false;
 100
 101   Thread discoverer = null;
 102   @Override
 103   public void run()
 104   {
 105     discoverer = Thread.currentThread();
 106     started = true;
 107     try
 108     {
 109       services = slivkaClient.getServices();
 110     } catch (IOException e)
 111     {
 112       throw new IOError(e);
 113     }
 114     finished = true;
 115   }
 116
 117   public static List<ServiceWithParameters> getServices()
 118   {
 119     SlivkaWSDiscoverer us = getInstance();
 120     if (us.services == null)
 121     {
 122       us.run();
 123     }
 124     return us.getServiceInstances();
 125   }
 126
 127   public boolean hasServices()
 128   {
 129     return finished == true && services != null && services.size() > 0;
 130   }
 131
 132   public boolean isRunning()
 133   {
 134     return discoverer != null && discoverer.isAlive();
 135   }
 136 }